ClearVolume
is an open source real-time live
3D visualization
Visualization or visualisation (see spelling differences) is any technique for creating images, diagrams, or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and ...
library designed for high-end volumetric
light sheet microscopes. ClearVolume enables the live visualization of microscope data - allowing the biologists to immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...
,
C/C++
The C and C++ programming languages are closely related but have many significant differences. C++ began as a fork of an early, pre- standardized C, and was designed to be mostly source-and-link compatible with C compilers of the time. Due to t ...
,
Python, or
LabVIEW
Laboratory Virtual Instrument Engineering Workbench (LabVIEW) is a system-design platform and development environment for a visual programming language from National Instruments.
The graphical language is named "G"; not to be confused with G- ...
based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the
FiJi/
ImageJ2/
KNIME
KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks ...
ecosystem.
See also
*
FiJi
*
KNIME
KNIME (), the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks ...
*
Light sheet fluorescence microscopy
Light or visible light is electromagnetic radiation that can be perceived by the human eye. Visible light is usually defined as having wavelengths in the range of 400–700 nanometres (nm), corresponding to frequencies of 750–420 terahe ...
*
Volume rendering
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set, typically a 3D scalar field.
A typical 3D data set is a group of 2D slice imag ...
References
{{reflist, refs=
[
{{cite journal
, author1=Royer, Loïc A , author2=Weigert, Martin , author3=Günther, Ulrik , author4=Maghelli, Nicola , author5=Jug, Florian , author6=Sbalzarini, Ivo F. , author7=Myers, Eugene W. , title = ClearVolume – Open-source live 3D visualization for light sheet microscopy.
, journal = Nature Methods
, volume = 12
, issue=6 , date = 2015
, url = http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3372.html
, doi = 10.1038/nmeth.3372 , pages=480–481 , pmid=26020498, s2cid=205423715
]
External links
Website of the open source ClearVolume project with links to the wiki, code repositories and issue tracking.
ClearVolume KNIME plugin project page.
ClearVolume FiJi plugin project page.
Computational science
Bioinformatics